Dear All Afew question about Pulling in Umberella Sampling 1-the goal of pulling is making some primary structures (in different distances) to do umberella sampling for each one of them. I can make these states by transporting my ligands along a vector to prepare these primary structures.Is this correct?Now I can do US for each one!without any need to doing pulling.
2-Why do we keep fix the relative orientation of Protein-ligand during the pulling ? I think changing the orientation of ligand during the pulling(suppose the protein is restrain) can chang our result? Because our umbrella sampling maintain this orientation too.am I right? Thanks in advance
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